TB-Profiler result

Run: ERR13252191
Summary

Run ID: ERR13252191

Sample name:

Date: 2025-03-09T19:26:23.737917

Number of reads: 2180384

Percentage reads mapped: 99.82

Median coverage: 114.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 1.0
lineage4.9 Euro-American (H37Rv-like) None 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Asp Assoc w R
isoniazid inhA p.Ile194Thr Uncertain significance Mutation from literature: doi: 10.1126/scitranslmed.3010597
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Gln497Lys Assoc w R
pyrazinamide pncA c.-301_*702del Assoc w R
streptomycin gid c.102delG Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-37G>T Assoc w R
cycloserine
ethionamide inhA p.Ile194Thr Uncertain significance Mutation from literature: doi: 10.1128/AAC.01028-15
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence Comment
rpoB 761139 p.His445Asp missense_variant 0.99 rifampicin Assoc w R
inhA 1674782 p.Ile194Thr missense_variant 1.0 ethionamide Uncertain significance Mutation from literature: doi: 10.1128/AAC.01028-15
isoniazid Uncertain significance Mutation from literature: doi: 10.1126/scitranslmed.3010597
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2287978 c.-301_*702del transcript_ablation 1.0 pyrazinamide Assoc w R
eis 2715369 c.-37G>T upstream_gene_variant 1.0 kanamycin Assoc w R
embB 4248002 p.Gln497Lys missense_variant 1.0 ethambutol Assoc w R
gid 4408100 c.102delG frameshift_variant 1.0 streptomycin Assoc w R
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoC 765461 p.Asn698Asp missense_variant 1.0 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 777217 p.Pro422Thr missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpR5 779147 p.Ser53Leu missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781638 p.Ser27Gly missense_variant 1.0 streptomycin Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1979c 2223724 c.-560C>G upstream_gene_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
pncA 2289887 c.-649_-647delCCG upstream_gene_variant 1.0 pyrazinamide Uncertain significance
eis 2714554 p.Asp260Ala missense_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
thyX 3067947 c.-2C>T upstream_gene_variant 1.0 para-aminosalicylic_acid Uncertain significance
thyA 3074169 p.Trp101* stop_gained 1.0 para-aminosalicylic_acid Uncertain significance
glpK 4139183 c.572dupG frameshift_variant 1.0 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R